Genome analysis of Chlorella vulgaris (CCAP 211/12) mutants provided insight into the molecular basis of chlorophyll deficiency

Chlorella vulgaris has a high photosynthetic efficiency and is used for commercial applications in foods. Targeted genetic engineering is currently challenging due to the lack of high-quality genomes. In this study, we investigated the differential chlorophyll content between wild type and chlorophyll-deficient mutants. We performed nuclear genome assembly, genetic variation, and gene expression analysis, resulting in a high-quality assembly for each genome with contig N50 > 2 Mb and genome completeness >97 %. Comparative genomic analysis showed that genomic characteristics and gene features were not different between the wild type and the four mutants. Minor genomic differences were observed between the wild type and the chlorophyll-deficient mutants, where five enzymatic steps were affected with downregulation leading to the chlorophyll-deficiency. The biggest effect was observed in the magnesium-protoporphyrin IX monomethyl ester cyclase (ChlE1) where large deletions led to a non-functional gene in three of the four mutants, and a clear change in structure for the last. The disrupted functionality of these genes, especially ChlE1, and change of expression of the pigment biosynthesis as a whole explains the chlorophyll-deficiency in our four mutant lines. The five sequenced C. vulgaris genomes provide a strong foundation to understand the molecular basis of chlorophyll biogenesis and for future genetic engineering and commercial strain development.